Scientists revive largest virus yet from 30,000-year-old permafrost

And it's a very strange beast. Fortunately, it only affects amoebas. We think.

The Pandoravirus (above) is physically similar, but shares very little in the way of genetic material with the newly discovered virus.

Up until recently, the line between viruses and cells seemed pretty simple: cells were big and carried everything they needed to live and grow. Viruses were tiny and only carried the genes they needed to take over their host cells; they relied on their hosts for most essential proteins.

That line got a bit blurry as we found parasitic and symbiotic cells with very stripped-down, minimalist genomes that wouldn't let them survive outside their hosts. But it's nearly been obliterated by the discovery of giant viruses—some of these have genomes that are larger than those of bacteria and carry many of the genes needed to copy DNA and translate it into proteins.

Further Reading

Scientists have now identified yet another giant virus, this time using a technique that sounds like it's straight out of a sci-fi horror flick: they thawed some 30,000-year-old permafrost and allowed any viruses present to infect some cells. Fortunately, the cells were amoebas, and this virus is overwhelmingly unlikely to present a threat to human health. But the fact that viruses could apparently survive so many centuries in the Siberian permafrost does lead the authors to suggest that the melting Arctic may pose an emerging disease risk.

The authors of the new paper, a mix of French and Russian researchers, identified the virus using a procedure that's incredibly simple: take a culture of amoebas (a strain that has been found in the permafrost) and put a bit of permafrost in with the culture. After that, it was a matter of waiting for something bad to happen to the amoebas.

The something bad in this case happened to be the explosion, or lysis, of the cells. A check of the culture showed the presence of a giant virus particle, shaped similarly to the Pandoravirus described in the article linked above. In terms of the sheer physical size of the virus, it's the largest one we've yet discovered. Because of its jug-like shape, the authors named it Pithovirus after a type of amphora used by Pandora (the namesake of the second largest virus).

However, there were some clear differences with Pandoravirus from the start. For example, the cork of the jug (their term, not mine) appears to contain some specialized fibers that are unlike anything seen in Pandoravirus. And the Pithovirus reproduces in a virus factory it sets up inside infected cells; the Pandoravirus takes over a cell's nucleus. (Viral factories are also set up by the first giant virus identified, Mimivirus, which looks physically distinct from these other two.)

Despite its giant physical size, Pithovirus carries a relatively small genome at only 600,000 DNA bases long. Some of the extra space inside the virus is taken up by the proteins needed to get the virus' replication started after infection (RNA transcription machinery). But the authors are at a bit of a loss to explain what all the extra space inside the virus' capsule might be used for.

The genome is also small in another sense: gene content. It encodes only 467 proteins, far fewer than the 1,000 to 2,500 genes carried by other giant viruses. Missing are the sorts of things that make the other giants unique among viruses: genes for translating RNA into proteins and others involved in energy metabolism. Also unusual is the presence of repetitive DNA. Viruses normally get rid of any unused DNA sequences, leaving most of their DNA taken up by protein-coding genes. Pithovirus has a large collection of nearly identical, non-protein coding sequences.

The authors suggest two options: either that the virus just needs the extra DNA as padding to make it large enough to work in its giant shell, or it has recently been invaded by some parasitic DNA and hasn't had the chance to get rid of it via evolution. (Although they can't rule out other possibilities right now.)

As far as the genes themselves, only a third are similar to anything we've ever seen before. And that third is divided roughly equally among similarities to genes from bacteria, the virus' eukaryotic host, and other viruses. All of which means that Pithovirus is a distinct type of virus from anything we've ever seen before. It does seem to be distantly related to some other viruses we've previously identified, but those aren't giants like this one.

So far, all of the giant viruses we've identified infect amoebas, and the authors chose to go this route when searching permafrost explicitly because it seemed safe. Anything that came out of the search was very unlikely to infect humans. But they consider the search itself a proof-of-principle: they took care not to contaminate the permafrost, which was still frozen when it was obtained. That means that the virus is very likely to have survived 32,000 years of deep freeze, which is how old the layer it came from appears to be.

All of which, the authors suggest, should be a warning. There are already humans living in areas with permafrost, and many more are expected to arrive there as the thawing Arctic makes exploitation of natural resources there much easier. The new find suggests that some of the new arrivals may potentially come in contact with infectious agents that have been out of circulation for tens of thousands of years. This doesn't mean the permafrost will necessarily be a hotbed of emerging diseases, but the authors argue that we might want to take the possibility seriously.

Eh, we are WAY overdue to start taking disease transmission reduction more seriously anyway.

With advances in automation, telecommunications, and entertainment we should REALLY have stopped packing humans together in little boxes to cough on each many times each day just to get them to, from and to take part in work, medicine, and entertainment.

The diseases from the antarctic that predate our position as massive ecological spam species are much less likely to be pandemic than the diseases that are currently circulating in our populations, missing only a few lucky mutations and a few plane trips to give us all a very bad time.

There is real but remote possibility that the permafrost will contain new (actually old) viruses harmful to humans.

But most viruses in the wild are uncatalogued and humans get mild or asymptomatic viral infections all the time without serious consequences, and without anyone knowing what the virus is. And surely there must be border zones where the permafrost is not so permanent and these soil viruses have already thawed and entered circulation in the ecological niche they live in.

Dangerous outbreaks for humans come from several things: when an infectious organism jumps the species barrier (Ebola, Marburg, Yersinia pestis, rabies,), and when known families of viruses mutate regularly as part of their long-term evolution (think influenza). There are also periodic scourges (leprosy, malaria, yellow fever) that come and go, these may locally or periodically mutate to become more or less virulent and pathogenic. Human populations are the natural reservoir for some pathogens, and animals or the environment are the natural reservoir for others. And of course there are dangerous pathogens in our environment (stagnant ponds; toxic algae; feces) that we've simply learned to avoid. Don't eat permafrost or rub it on an open would and you should be just fine.

Ah, yes, I was wondering why the first amphora type viruses didn't show any viral factory. If these giants are simplified parasites evolved out of cells, which already their dsDNA and complexity suggest, the viral factory should be homologous with the original cell. The virions (viral particles) are then analogous, maybe even homologous, with spores.

Interesting to see how virions are encapsulated though. The generic virions has different capsule proteins and stacking arrangements that I understand are all one way or other phylogenetically related to cellular membrane pore proteins and how they stack similar units to build structures.

The amphora is very different, more reminding of a whole cell encapsulation rather than chosen (possibly remnant) pieces.

Maybe the amphora is what decides the space rather than the usually compressed virion genome. RNA viruses may even work as injection needles, and I believe they have now found one that uses a homolog to a bacterial molecular assemblage needle for sharing plasmids. The amphora instead seems useful as soon as you have eukaryotes that are large enough to be tricked to swallow you for attempted feeding.

I assume these viruses could only evolve after eukaryotes got large enough. Too bad that we have only been able to date the mitochondrial endosymbiosis with eukaryotes (~ 1 Ga bp). That doesn't necessarily bear on cell size as much as genome size. But maybe, just maybe, these viruses are the newest viral clade on the block.

Quote:

Fortunately, it only affects amoebas. We think.

I understand that the giant viruses of the Mimi type were first seen in amoebas that had infested eyes of human patients. But nobody at the time understood that it was viruses, not bacteria, they were looking at.

We humans are like chinese boxes, arent' we? Humans with amoebas with giant viruses, possibly with Sputnik analog viroids... (I'm sure one could cram in a parasite between human and amoeba, too.) =D

The potential to do good has always outweighed the potential to do bad in the eyes of the scientific community, whether it is a right or wrong perspective. Imagine if the discovery of these monolithic beasts led to a new level of understanding of viral replication. Or perhaps a new vehicle in the treatment of evasive diseases plaguing people by using them as delivery vessels?

Remember, it isn't the research you need to fear. It is the people paying the people conducting the research. There's always a wallet behind every well intentioned scientist and engineer looking to make a profit off their work.

There is real but remote possibility that the permafrost will contain new (actually old) viruses harmful to humans.

But most viruses in the wild are uncatalogued and humans get mild or asymptomatic viral infections all the time without serious consequences, and without anyone knowing what the virus is. And surely there must be border zones where the permafrost is not so permanent and these soil viruses have already thawed and entered circulation in the ecological niche they live in.

Dangerous outbreaks for humans come from several things: when an infectious organism jumps the species barrier (Ebola, Marburg, Yersinia pestis, rabies,), and when known families of viruses mutate regularly as part of their long-term evolution (think influenza). There are also periodic scourges (leprosy, malaria, yellow fever) that come and go, these may locally or periodically mutate to become more or less virulent and pathogenic. Human populations are the natural reservoir for some pathogens, and animals or the environment are the natural reservoir for others. And of course there are dangerous pathogens in our environment (stagnant ponds; toxic algae; feces) that we've simply learned to avoid. Don't eat permafrost or rub it on an open would and you should be just fine.

Yes, but currently Humans have been to almost every corner of the earth, so we've evolved to some extent with existing viruses. You forget the effect of Europeans entering the New World and the deadly toll the viruses they carried with them took on the local populace. That could very well happen once a substantial amount of permafrost has melted.

I'm having a surprising amount of trouble finding this paper. The DOI doesn't work, nor does the link on the NY Times article (http://www.nytimes.com/2014/03/04/scien ... vived.html) nor does the link on Nature's writeup. These are publications that don't usually make those mistakes. (I know, I know! Internet commenter who tries to actually read the original article before commenting!)

Was the paper held back for last-minute corrections? That's not something that usually happens with peer-reviewed papers, and if it's what happened, it's not a minor thing.

I'm having a surprising amount of trouble finding this paper. The DOI doesn't work, nor does the link on the NY Times article (http://www.nytimes.com/2014/03/04/scien ... vived.html) nor does the link on Nature's writeup. These are publications that don't usually make those mistakes. (I know, I know! Internet commenter who tries to actually read the original article before commenting!)

Was the paper held back for last-minute corrections? That's not something that usually happens with peer-reviewed papers, and if it's what happened, it's not a minor thing.

Maybe it was one of those computer generated nonsense articles. (Probably not, but I didn't see anything on ars about that situation and thought I'd see if I could get a discussion about that.)

I can't choose. Mother Abigail or Randall Flagg? There are pros and cons to consider there.....

the dark man is just so much more exciting! Vegas or Boulder free zone?

Considering you get crucified for smoking crack or getting liquored up and saying the wrong thing in The Dark Man's Vegas, I think I'll roll on over to Boulder, please and thank you! I'd rather get Jesus'ed at now and again by Mother Abagail then nailed up!